/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
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- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
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- * the papers on the package - you can find them in the top README file.
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*
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+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
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- * Green Red Orange Magenta Azure Cyan Skyblue
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include <ctype.h>
-#include "string2.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "tpxio.h"
-#include "physics.h"
-#include "index.h"
-#include "smalloc.h"
-#include "calcgrid.h"
-#include "nrnb.h"
-#include "coulomb.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/coulomb.h"
#include "gstat.h"
-#include "matio.h"
#include "gmx_ana.h"
-#include "names.h"
+#include "gromacs/legacyheaders/names.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void check_box_c(matrix box)
{
char **grpname;
int *isize, isize_cm = 0, nrdf = 0, max_i, isize0, isize_g;
atom_id **index, *index_cm = NULL;
-#if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
- long long int *sum;
-#else
- double *sum;
-#endif
+ gmx_int64_t *sum;
real t, rmax2, cut2, r, r2, r2ii, invhbinw, normfac;
real segvol, spherevol, prev_spherevol, **rdf;
rvec *x, dx, *x0 = NULL, *x_i1, xi;
invvol_sum = 0;
if (bPBC && (NULL != top))
{
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
}
do
}
nframes++;
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
if (bPBC && (NULL != top))
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
do_view(oenv, fnRDF, NULL);
{
fprintf(fp, "%10g %10g\n", i*0.5, hq[i]);
}
- ffclose(fp);
+ gmx_ffclose(fp);
do_view(oenv, fnHQ, NULL);
sfree(hq);
sfree(integrand);
}
fprintf(fp, "\n");
}
- ffclose(fp);
+ gmx_ffclose(fp);
sfree(sum);
do_view(oenv, fnCNRDF, NULL);
"scattering. The most common way to describe liquid structure is by a",
"radial distribution function. However, this is not easy to obtain from",
"a scattering experiment.[PAR]",
- "[TT]g_rdf[tt] calculates radial distribution functions in different ways.",
+ "[THISMODULE] calculates radial distribution functions in different ways.",
"The normal method is around a (set of) particle(s), the other methods",
"are around the center of mass of a set of particles ([TT]-com[tt])",
"or to the closest particle in a set ([TT]-surf[tt]).",
{ efXVG, "-hq", "hq", ffOPTWR },
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
if (bCM || closet[0][0] != 'n' || rdft[0][0] == 'm' || rdft[0][6] == 'm')
{
bCM, closet[0], rdft, bXY, bPBC, bNormalize, cutoff, binwidth, fade, ngroups,
oenv);
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff